5CUU | pdb_00005cuu

Crystal structure of Trypanosoma cruzi Vacuolar Soluble Pyrophosphatases in complex with bisphosphonate inhibitor BPH-1260

• PDB DOI: https://doi.org/10.2210/pdb5CUU/pdb

• Classification: METAL BINDING PROTEIN
• Organism(s): Trypanosoma cruzi
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2015-07-25 Released: 2016-03-02 
• Deposition Author(s): Liu, W.D., Yang, Y.Y., Ko, T.P., Zheng, Y.Y., Chen, C.C., Guo, R.T.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.96 Å
• R-Value Free: 
  0.274 (Depositor), 0.259 (DCC) 
• R-Value Work: 
  0.194 (Depositor), 0.190 (DCC) 

Starting Model: experimental

Literature

Crystal structure of Trypanosoma cruzi protein in complex with ligand

Yang, Y.Y., Ko, T.P., Zheng, Y.Y., Liu, W.D., Chen, C.C., Guo, R.T.

(2016) ACS Chem Biol 

Biological Assembly 1  

Global Symmetry: Dihedral - D2  (Explore in 3D)
Global Stoichiometry: Homo 4-mer - A4 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 96.94 kDa 
• Atom Count: 6,377 
• Modeled Residue Count: 757 
• Deposited Residue Count: 828 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Acidocalcisomal pyrophosphatase	A, B	414	Trypanosoma cruzi	Mutation(s): 0  EC: 3.6.1.1
UniProt
Find proteins for Q4JH30 (Trypanosoma cruzi) Explore Q4JH30  Go to UniProtKB:  Q4JH30

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
4GA	E [auth A], H [auth B]	1-butyl-3-(2-hydroxy-2,2-diphosphonoethyl)-1H-imidazol-3-ium C9 H19 N2 O7 P2 JCMWHMYRNYPQAZ-UHFFFAOYSA-O
MLT	C [auth A], D [auth A], G [auth B]	D-MALATE C4 H6 O5 BJEPYKJPYRNKOW-UWTATZPHSA-N
MG	F [auth A], I [auth B]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.96 Å
• R-Value Free:  0.274 (Depositor), 0.259 (DCC) 
• R-Value Work:  0.194 (Depositor), 0.190 (DCC) 

Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 100.775	α = 90
b = 102.63	β = 90
c = 158.834	γ = 90

Software Package:

Software Name	Purpose
HKL-2000	data scaling
CNS	refinement
PDB_EXTRACT	data extraction
HKL-2000	data reduction
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2016-03-02 
Deposition Author(s): Liu, W.D., Yang, Y.Y., Ko, T.P., Zheng, Y.Y., Chen, C.C., Guo, R.T.

Revision History  

• Version 1.0: 2016-03-02
  Type: Initial release
  
• Version 1.1: 2016-03-09
  Changes: Data collection
• Version 1.2: 2023-11-08
  Changes: Data collection, Database references, Derived calculations, Refinement description